Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.15.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00914	0.876
27DAP/17DAP	1.39036	0.73
39DAP/27DAP	1.05286	1
41DAP/39DAP	1.03856	0.904
42DAP/41DAP	0.84484	0.774
43DAP/42DAP	1.12498	0.875
47DAP/43DAP	1.07416	1
52DAP/47DAP	0.81365	0.513
57DAP/52DAP	1.25058	0.93

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80189	0.036
17DAP/reference	1.07288	0.161
27DAP/reference	1.01469	0.863
39DAP/reference	1.04895	0.593
41DAP/reference	0.99782	1
42DAP/reference	0.91997	0.059
43DAP/reference	0.99403	0.84
47DAP/reference	1.0064	0.764
52DAP/reference	1.03647	1
57DAP/reference	1.07532	0.044

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84458	0.148
27DAP/17DAP	1.23707	0.541
39DAP/27DAP	0.99088	0.932
41DAP/39DAP	1.24177	0.579
42DAP/41DAP	1.0621	0.727
43DAP/42DAP	0.93444	0.597
47DAP/43DAP	0.97349	0.902
52DAP/47DAP	0.80524	0.472
57DAP/52DAP	1.05157	0.957
57DAP/7DAP	7.12235	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95092	0.361
17DAP/reference	0.83504	0.024
27DAP/reference	0.88824	0.076
39DAP/reference	0.85809	0.025
41DAP/reference	0.90877	0.166
42DAP/reference	0.62992	0.066
43DAP/reference	0.79915	0.017
47DAP/reference	1.04707	1
52DAP/reference	0.70965	0.024
57DAP/reference	0.78077	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02581	0.741
17DAP/reference	1.02144	0.584
27DAP/reference	0.9839	0.576
39DAP/reference	0.88968	0.147
41DAP/reference	0.91607	0.1
42DAP/reference	0.99698	0.655
43DAP/reference	0.98606	0.692
47DAP/reference	1.05079	0.301
52DAP/reference	0.96469	0.28
57DAP/reference	0.93871	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83757	0.032
17DAP/reference	0.90927	0.162
27DAP/reference	0.91919	0.302
39DAP/reference	0.74632	0.015
41DAP/reference	0.84874	0.05
42DAP/reference	0.80771	0.041
43DAP/reference	0.73104	0.15
47DAP/reference	0.98139	0.494
52DAP/reference	0.8703	0.208
57DAP/reference	0.86033	0.102

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09957	0.966
26DAP/20DAP	1.14721	0.464
34DAP/26DAP	0.8509	0.816
51DAP/34DAP	0.80982	0.624
52DAP/51DAP	1.20025	0.708
53DAP/52DAP	1.21031	0.797
55DAP/53DAP	0.92781	0.663
57DAP/55DAP	1.03471	1
62DAP/57DAP	1.24806	0.393
68DAP/62DAP	1.02499	1
68DAP/14DAP	1.35571	0.366

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01568	1

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70035	0.189
Mature Green Tomato/Ripe Tomato	1.02915	0.66
Immature Eggplant/Mature Eggplant	3.13808	0.05
Ripe Pepper/Ripe Tomato	4.4785	1
Mature Eggplant/Ripe Tomato	0.72053

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0141	1
1-1-2/M82	0.97194	1
12-2/M82	N/A	N/A
12-4/M82	0.60071	0.619
1-3/M82	1.91593
2-1-1/M82	1.01576
2-1/M82	2.4389
2-6/M82	1.49618	0.505
3-2/M82	1.02676	0.967
4-1-1/M82	N/A	N/A
4-1/M82	0.75177	0.737
4-3-2/M82	1.05447	1
4-3/M82	1.51039	1
5-3/M82	0.94416	1
6-2/M82	N/A	N/A
6-3/M82	0.65037	0.982
7-1/M82	0.90882
7-2/M82	2.59762
9-3-2/M82	0.90557	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.72847
IL2-6/WTpooled	0.79925	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.05204	1
IL12-4/WTpooled	1.02827	1
IL1-4/WTpooled	0.96275
WT/WTpooled	1.01083	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.6214	0.222

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.20531	0.875
DC3000/delta hrp 6h	0.95419	0.95
DC3000/delta hrp 12h	0.95451	1
DC3000/delta hrp 24h	1.40407	0.107

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.55583
DC3000 delta B/DC3000 delta AB	1.45361	0.121

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.07319	1
Exp 36h	1.41082	0.693
Exp 60h	1.0754	1

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.1146	1
Var 0h	1.08788	1
Var 12h I row2-row1	1.01394	1
Var 12h NI row2-row1	1.10898	1
Var 36h I row2-row1	0.97231	1
Var 36h NI row2-row1	0.67808	0.45
Var 60h I row2-row1	0.82673	0.285
Var 60h NI row2-row1	0.75964	0.63
Time course 0hI-0hNI	0.8888	0.226
Time course 12hI-12hNI	1.15614	0.122
Time course 36hI-36hNI	2.04243	0.005
Time course 60hI-60hNI	3.31534	0.008

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.94703	0.265
transgenic ySAMdc/azygous control (breaker)	0.83766	0.49
transgenic ySAMdc/azygous control (red)	0.94567	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12694	0.046

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87806	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.81725	1
Manapal/WT (break)	0.95735	1
Manapal/WT (red)	2.59474	0.413